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Unraveling the genetics of underwater caddisfly silk.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-31 DOI: 10.1016/j.tig.2025.01.004
Samantha Standring, Jacqueline Heckenhauer, Russell J Stewart, Paul B Frandsen
{"title":"Unraveling the genetics of underwater caddisfly silk.","authors":"Samantha Standring, Jacqueline Heckenhauer, Russell J Stewart, Paul B Frandsen","doi":"10.1016/j.tig.2025.01.004","DOIUrl":"https://doi.org/10.1016/j.tig.2025.01.004","url":null,"abstract":"<p><p>Hundreds of thousands of arthropod species use silk to capture prey, build protective structures, or anchor eggs. While most silk-producers are terrestrial, caddisflies construct silken capture nets and portable cases in aquatic environments. Given the potential practical applications of this underwater bioadhesive, there is an emerging body of research focused on understanding the evolution of the genetic architecture of aquatic silk. This research has unveiled molecular adaptations specific to caddisfly silk, such as extensive phosphorylation of the primary silk protein and the existence of numerous unique accessory silk proteins. We discuss the molecular evolution of caddisfly silk genes, how they interact with the environment, and suggest future directions for caddisfly silk genetics research.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic buffering mechanisms in SNF2-family translocases.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-30 DOI: 10.1016/j.tig.2025.01.005
Sumedha Agashe, Alessandro Vindigni
{"title":"Genetic buffering mechanisms in SNF2-family translocases.","authors":"Sumedha Agashe, Alessandro Vindigni","doi":"10.1016/j.tig.2025.01.005","DOIUrl":"https://doi.org/10.1016/j.tig.2025.01.005","url":null,"abstract":"<p><p>SNF2-family DNA translocases, a large family of ATPases, have poorly defined roles in genomic stability. In a recent study, Feng et al. identified a synthetic lethal interaction between the SNF2 translocase SMARCAL1 and Fanconi anemia (FA) group M (FANCM), revealing a new genetic buffering mechanism that maintains genome stability by aiding DNA replication at loci enriched in simple repeats.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Emerging insights into the genetics and evolution of human same-sex sexual behavior.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-28 DOI: 10.1016/j.tig.2024.12.005
Thomas Felesina, Brendan P Zietsch
{"title":"Emerging insights into the genetics and evolution of human same-sex sexual behavior.","authors":"Thomas Felesina, Brendan P Zietsch","doi":"10.1016/j.tig.2024.12.005","DOIUrl":"https://doi.org/10.1016/j.tig.2024.12.005","url":null,"abstract":"<p><p>Thanks to twin studies, it has been known for decades that human same-sex sexual behavior (SSB) has a substantial heritable component. However, only recently have large genome-wide association studies (GWAS) begun to illuminate the complex genetics involved. These studies have established that SSB is influenced by many common genetic variants, each with tiny but cumulative effects. The evolutionary explanation for the persistence of genetic variants associated with SSB, despite their apparent fitness costs, remains uncertain. In this review, we synthesize advances in understanding the genetic and evolutionary bases of SSB, while identifying the many areas in which we still have much to learn.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transcription and epigenetic factor dynamics in neuronal activity-dependent gene regulation.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-28 DOI: 10.1016/j.tig.2024.12.008
Noriyuki Sugo, Yuri Atsumi, Nobuhiko Yamamoto
{"title":"Transcription and epigenetic factor dynamics in neuronal activity-dependent gene regulation.","authors":"Noriyuki Sugo, Yuri Atsumi, Nobuhiko Yamamoto","doi":"10.1016/j.tig.2024.12.008","DOIUrl":"https://doi.org/10.1016/j.tig.2024.12.008","url":null,"abstract":"<p><p>Neuronal activity, including sensory-evoked and spontaneous firing, regulates the expression of a subset of genes known as activity-dependent genes. A key issue in this process is the activation and accumulation of transcription factors (TFs), which bind to cis-elements at specific enhancers and promoters, ultimately driving RNA synthesis through transcription machinery. Epigenetic factors such as histone modifiers also play a crucial role in facilitating the specific binding of TFs. Recent evidence from epigenome analyses and imaging studies have revealed intriguing mechanisms: the default chromatin structure at activity-dependent genes is formed independently of neuronal activity, while neuronal activity modulates spatiotemporal dynamics of TFs and their interactions with epigenetic factors (EFs). In this article we review new insights into activity-dependent gene regulation that affects brain development and plasticity.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Revealing microRNA regulation in single cells.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-24 DOI: 10.1016/j.tig.2024.12.009
Ranjan K Maji, Matthias S Leisegang, Reinier A Boon, Marcel H Schulz
{"title":"Revealing microRNA regulation in single cells.","authors":"Ranjan K Maji, Matthias S Leisegang, Reinier A Boon, Marcel H Schulz","doi":"10.1016/j.tig.2024.12.009","DOIUrl":"https://doi.org/10.1016/j.tig.2024.12.009","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) are key regulators of gene expression and control cellular functions in physiological and pathophysiological states. miRNAs play important roles in disease, stress, and development, and are now being investigated for therapeutic approaches. Alternative processing of miRNAs during biogenesis results in the generation of miRNA isoforms (isomiRs) which further diversify miRNA gene regulation. Single-cell RNA-sequencing (scsRNA-seq) technologies, together with computational strategies, enable exploration of miRNAs, isomiRs, and interacting RNAs at the cellular level. By integration with other miRNA-associated single-cell modalities, miRNA roles can be resolved at different stages of processing and regulation. In this review we discuss (i) single-cell experimental assays that measure miRNA and isomiR abundances, and (ii) computational methods for their analysis to investigate the mechanisms of miRNA biogenesis and post-transcriptional regulation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143043201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chromatin accessibility provides a window into the genetic etiology of human brain disease.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-23 DOI: 10.1016/j.tig.2025.01.001
Jaroslav Bendl, John F Fullard, Kiran Girdhar, Pengfei Dong, Roman Kosoy, Biao Zeng, Gabriel E Hoffman, Panos Roussos
{"title":"Chromatin accessibility provides a window into the genetic etiology of human brain disease.","authors":"Jaroslav Bendl, John F Fullard, Kiran Girdhar, Pengfei Dong, Roman Kosoy, Biao Zeng, Gabriel E Hoffman, Panos Roussos","doi":"10.1016/j.tig.2025.01.001","DOIUrl":"10.1016/j.tig.2025.01.001","url":null,"abstract":"<p><p>Neuropsychiatric and neurodegenerative diseases have a significant genetic component. Risk variants often affect the noncoding genome, altering cis-regulatory elements (CREs) and chromatin structure, ultimately impacting gene expression. Chromatin accessibility profiling methods, especially assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), have been used to pinpoint disease-associated SNPs and link them to affected genes and cell types in the brain. The integration of single-cell technologies with genome-wide association studies (GWAS) and transcriptomic data has further advanced our understanding of cell-specific chromatin dynamics. This review discusses recent findings regarding the role played by chromatin accessibility in brain disease, highlighting the need for high-quality data and rigorous computational tools. Future directions include spatial chromatin studies and CRISPR-based functional validation to bridge genetic discovery and clinical applications, paving the way for targeted gene-regulatory therapies.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143043200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
DEAD/DEAH-box RNA helicases shape the risk of neurodevelopmental disorders. 死亡/死亡盒RNA解旋酶影响神经发育障碍的风险。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-18 DOI: 10.1016/j.tig.2024.12.006
Chiara Fiorenzani, Adele Mossa, Silvia De Rubeis
{"title":"DEAD/DEAH-box RNA helicases shape the risk of neurodevelopmental disorders.","authors":"Chiara Fiorenzani, Adele Mossa, Silvia De Rubeis","doi":"10.1016/j.tig.2024.12.006","DOIUrl":"https://doi.org/10.1016/j.tig.2024.12.006","url":null,"abstract":"<p><p>The DEAD/DEAH-box family of RNA helicases (RHs) is among the most abundant and conserved in eukaryotes. These proteins catalyze the remodeling of RNAs to regulate their splicing, stability, localization, and translation. Rare genetic variants in DEAD/DEAH-box proteins have recently emerged as being associated with neurodevelopmental disorders (NDDs). Analyses in cellular and animal models have uncovered fundamental roles for these proteins during brain development. We discuss the genetic and functional evidence that implicates DEAD/DEAH-box proteins in brain development and NDDs, with a focus on how structural insights from paralogous genes can be leveraged to advance our understanding of the pathogenic mechanisms at play.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143016594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Conserved dynamics of natal down-to-juvenile feather transition. 幼崽羽毛过渡的保守动力学。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-09 DOI: 10.1016/j.tig.2024.12.007
Marie Manceau
{"title":"Conserved dynamics of natal down-to-juvenile feather transition.","authors":"Marie Manceau","doi":"10.1016/j.tig.2024.12.007","DOIUrl":"https://doi.org/10.1016/j.tig.2024.12.007","url":null,"abstract":"<p><p>Despite the ecological importance of the feather cover during early avian life, the events controlling the transition from natal down to juvenile feathers are poorly understood. Chen et al. demonstrate that this transition is characterized by a series of morphological and molecular changes strikingly conserved between precocial and altricial species.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genomic language models: opportunities and challenges. 基因组语言模型：机遇与挑战。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-02 DOI: 10.1016/j.tig.2024.11.013
Gonzalo Benegas, Chengzhong Ye, Carlos Albors, Jianan Canal Li, Yun S Song
{"title":"Genomic language models: opportunities and challenges.","authors":"Gonzalo Benegas, Chengzhong Ye, Carlos Albors, Jianan Canal Li, Yun S Song","doi":"10.1016/j.tig.2024.11.013","DOIUrl":"https://doi.org/10.1016/j.tig.2024.11.013","url":null,"abstract":"<p><p>Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of natural language processing is to understand sequences of words, a major objective in biology is to understand biological sequences. Genomic language models (gLMs), which are LLMs trained on DNA sequences, have the potential to significantly advance our understanding of genomes and how DNA elements at various scales interact to give rise to complex functions. To showcase this potential, we highlight key applications of gLMs, including functional constraint prediction, sequence design, and transfer learning. Despite notable recent progress, however, developing effective and efficient gLMs presents numerous challenges, especially for species with large, complex genomes. Here, we discuss major considerations for developing and evaluating gLMs.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The good, the bad, and Neanderthalic immunity. 好的、坏的和尼安德特人的免疫力。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-01 Epub Date: 2024-11-14 DOI: 10.1016/j.tig.2024.10.010
Susannah Selber-Hnatiw, Sirui Zhou
{"title":"The good, the bad, and Neanderthalic immunity.","authors":"Susannah Selber-Hnatiw, Sirui Zhou","doi":"10.1016/j.tig.2024.10.010","DOIUrl":"10.1016/j.tig.2024.10.010","url":null,"abstract":"<p><p>Introgression with archaic hominins and subsequent natural selection has shaped the immune system of modern humans. Recently, Sun et al. investigated the immunity advantages of a Neanderthalic variant in the membrane-bound immunoglobulin G1 (IGHG1) gene, activating pathogen-specific antibody production toward modern threats yet conversely increasing the risk of autoimmune diseases.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"6-8"},"PeriodicalIF":13.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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